International Journal of Molecular Sciences

Journal Browser

► Journal Browser

Special Issue Information

Dear Colleagues,

Molecular docking is gaining increased interest in drug design approaches, especially considering its noteworthy potentialities in performing successful virtual screening campaigns. Currently available computing resources allow for simulations involving huge molecular libraries on extended panels of targets in a reasonable time, and these extremely extended simulations appear to be particularly fruitful in the field of multi-target ligand design as well as in the repurposing studies. Clearly, these powerful simulations require new algorithms and new methodological approaches to optimize their performances and to match the advancements in the hardware architectures. Molecular docking requires continuous improvements especially focused on the algorithms for scoring function and pose evaluation. Molecular docking is often combined with other computational approaches to further improve the reliability of the obtained results in terms of both computed complexes and predictive power, and, in this context, machine learning techniques can offer new avenues with which to improve docking simulations and virtual screening campaigns.

On these grounds, this Special Issue seeks manuscripts dealing with novel approaches of molecular docking in drug design by considering both methodological and applicative studies with a view to offering a picture of the areas in which docking simulations can have an ever-increasing impact in the drug discovery pipeline, as well as with the new trends that will impact on such a field in the next future.

Prof. Dr. Giulio Vistoli
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Related Special Issues

Published Papers (1 paper)

Research

16 pages, 5943 KiB

Open AccessArticle

In Silico Search for Drug Candidates Targeting the PAX8–PPARγ Fusion Protein in Thyroid Cancer

by Kaori Sakaguchi, Yoshio Okiyama and Shigenori Tanaka

Int. J. Mol. Sci. 2024, 25(10), 5347; https://doi.org/10.3390/ijms25105347 - 14 May 2024

Viewed by 159

Abstract

The PAX8/PPARγ rearrangement, producing the PAX8–PPARγ fusion protein (PPFP), is thought to play an essential role in the oncogenesis of thyroid follicular tumors. To identify PPFP-targeted drug candidates and establish an early standard of care for thyroid tumors, we performed ensemble-docking-based compound screening. Specifically, we investigated the pocket structure that should be adopted to search for a promising ligand compound for the PPFP; the position of the ligand-binding pocket on the PPARγ side of the PPFP is similar to that of PPARγ; however, the shape is slightly different between them due to environmental factors. We developed a method for selecting a PPFP structure with a relevant pocket and high prediction accuracy for ligand binding. This method was validated using PPARγ, whose structure and activity values are known for many compounds. Then, we performed docking calculations to the PPFP for 97 drug or drug-like compounds registered in the DrugBank database with a thiazolidine backbone, which is one of the characteristics of ligands that bind well to PPARγ. Furthermore, the binding affinities of promising ligand candidates were estimated more reliably using the molecular mechanics Poisson–Boltzmann surface area method. Thus, we propose promising drug candidates for the PPFP with a thiazolidine backbone. Full article

(This article belongs to the Special Issue New Avenues in Molecular Docking for Drug Design 2023)

► Show Figures